Amber14 Installation
You can download AmberTools14.tar.bz2 for free, Amber14.tar.bz2 is not free but only featured PMEMD, if you just want to use sander, free version is enough.
1. edit /etc/bashrc
export AMBERHOME=/path/to/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
2. untar files
tar xvf AmerTools14.tar.bz2
tar xvf Amber14.tar.bz2
(sudo dnf install libXt-devel libXext-devel libX11-devel libICE-devel libSM-devel flex patch bzip2-devel zlib-devel on fedora23)
also check tcsh gcc-c++ gcc-gfortran python-devel mpich mpich-devel are properly installed
if you want to install with cuda 7.X with gcc version >4.9
edit the following file and mark off error with "//"
/usr/local/cuda-7.*/include/host_config.h
#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9) //#error -- unsupported GNU version! gcc 4.10 and up are not supported! #endif /* __GNUC__> 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9) */
3. configure & compile
3.1 MPI only version
cd /path/to/amber14
./configure -mpi gnu
make sure you source the /../../amber.sh before next step
make install
test
export DO_PARALLEL="mpirun -np 6"(some of the program requires less than 6 threads)
make test.parallel
3.2 Compile with gpu support
export CUDA_HOME=/....
export PATH=$PATH:$CUDA_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64
./configure -cuda gnu
make install
make test
3.3 If you have more than one graphic card, compile cuda.MPI version
./configure -cuda -mpi gnu
make install
3.4 no matter what compile serial version is a must, so we can get all the tools we need
./configure gnu
make install
make test.seiral
Install matplotlib,Tkinter
yum install python-matplotlib
yum install tkinte
**gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory (fedora 24)
solution:
sudo dnf install redhat-rpm-config-40-2.fc24.noarch
amber mdcrd to dcd:
cpptraj -p topology.parm7 -y input.mdcrd -x output.dcd
to pdb
cpptraj -p water_box.prmtop -y md.rst -x md.pdb
extract frames from mdcrd file
create an input file, *.in
|
parm morc16_micelle.prmtop trajin mdcrd 1 300 10 trajout tmp.mdcrd netcdf |
cpptraj -i *.in
[References]
http://jswails.wikidot.com/installing-amber14-and-ambertools14
http://ambermd.org/doc/OFF_file_format.txt
http://www.cryst.bbk.ac.uk/PPS2/course/section7/os_non.html